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annotate SpyBOAT.xml @ 0:1d62de03829d draft

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"planemo upload commit c6cd06d44dce1eef9136017289d362f144687dc1"
author gregor.m
date Mon, 23 Nov 2020 13:31:47 +0000
parents
children 97fd3740f41c
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1 <tool id="SpyBOAT" name="SpyBOAT" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="0.0.2">spyboat</requirement>
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4 </requirements>
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5 <version_command>python $__tool_directory__/cl_wrapper.py --version</version_command>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python $__tool_directory__/cl_wrapper.py
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8 --input_path '$movie'
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9 #if $gauss_sigma:
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10 --gauss_sigma $gauss_sigma
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11 #end if
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12 #if $rescale_factor:
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13 --rescale $rescale_factor
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14 #end if
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15
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16 #if $masking.selection_mode == "create_fixed_mask":
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17 --masking fixed
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18 --mask_frame $masking.mask_frame
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19 --mask_thresh $masking.mask_thresh
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20 #else if $masking.selection_mode == "create_dynamic_mask":
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21 --masking dynamic
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22 --mask_thresh $masking.mask_thresh
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23 #end if
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24
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25 --dt $dt
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26 --Tmin $tmin
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27 --Tmax $tmax
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28 --nT $nt
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29 #if $tcutoff
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30 --Tcutoff $tcutoff
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31 #end if
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32 #if $win_size:
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33 --win_size $win_size
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34 #end if
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35
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36 --phase_out $phase_out
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37 --period_out $period_out
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38 --power_out $power_out
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39 --amplitude_out $amplitude_out
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40 #if $preprocessed_out:
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41 --preprocessed_out $preprocessed_out
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42 #end if
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43
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44 --html_fname $html_out
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45 --report_img_path '$html_out.extra_files_path'
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46
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47 --ncpu "\${GALAXY_SLOTS:-8}"
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48 > $log
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49
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50 ]]></command>
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51 <inputs>
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52 <param name="movie" type="data" format="tiff" label="Movie to process"
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53 help="Select a movie to Wavelet process"/>
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54
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55 <!--
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56 The following Wavelet parameters must have the same numerical type as defined in the
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57 argparse parser in cl_wrapper.py
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58 -->
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59
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60 <param name="gauss_sigma" type="float" label="Sigma"
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61 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired." optional="true">
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62 <validator type="in_range" min="0" max="9999999"/>
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63 </param>
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64
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65 <param name="rescale_factor" type="integer" value="" label="Rescale factor"
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66 help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling"
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67 optional="true">
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68 <validator type="in_range" min="0" max="99"/>
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69 </param>
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70
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71 <conditional name="masking">
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72 <param label="Masking the output" name="selection_mode" type="select" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output">
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73 <option selected="true" value="no_masking">No masking</option>
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74 <option value="create_fixed_mask">Create a fixed mask</option>
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75 <option value="create_dynamic_mask">Create a dynamic mask</option>
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76 </param>
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77 <when value="create_fixed_mask">
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78 <param name="mask_frame" type="integer" value="1" label="Create mask from frame"
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79 help="Creates a fixed mask from the chosen frame of the input movie.">
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80 <validator type="in_range" min="1" max="99999"/>
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81 </param>
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82 <param name="mask_thresh" type="float" value="0" label="Threshold"
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83 help="All pixels below this threshold will be masked in the output.">
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84 <validator type="in_range" min="0" max="999999"/>
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85 </param>
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86 </when>
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87 <when value="create_dynamic_mask">
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88 <param name="mask_thresh" type="float" value="0" label="Threshold"
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89 help="For each frame of the input, all pixels below this threshold will be masked in the output.">
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90 <validator type="in_range" min="0" max="999999"/>
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91 </param>
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92 </when>
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93 </conditional>
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94
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95 <param name="dt" type="float" value="1" label="Sampling interval" help="Time span between two frames">
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96 <validator type="in_range" min="0" max="9999999"/>
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97 </param>
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98 <param name="tmin" type="float" value="2" label="Smallest period" help="Minimal period to scan for">
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99 <validator type="in_range" min="0" max="9999999"/>
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100 </param>
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101
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102 <param name="tmax" type="float" value="30" label="Largest period"
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103 help="Maximal period to scan for">
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104 <validator type="in_range" min="0" max="9999999"/>
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105 </param>
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106
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107 <param name="nt" type="integer" value="150" label="Number of periods to scan for"
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108 help="Determines period resolution of the Wavelet power spectra">
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109 <validator type="in_range" min="0" max="9999999"/>
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110 </param>
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111
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112 <param name="tcutoff" type="float" value="40" label="Tcutoff"
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113 help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true">
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114 <validator type="in_range" min="0" max="9999999"/>
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115 </param>
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116
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117 <param name="win_size" type="float" value="" label="Sliding window size"
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118 help="Window size for amplitude envelope estimation, leave blank to disable normalization "
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119 optional="true">
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120 <validator type="in_range" min="0" max="9999999"/>
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121 </param>
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122
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123 <conditional name="save_preprocessed">
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124 <param label="Save preprocessed input" name="selection" type="select" help="Save the blurred/rescaled input to history? ">
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125 <option selected="true" value="No">No</option>
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126 <option value="Yes">Yes</option>
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127 </param>
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128 </conditional>
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129 </inputs>
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130
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131 <outputs>
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132 <data name="phase_out" format="tiff" label="phase_${movie.name}"/>
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133 <data name="period_out" format="tiff" label="period_${movie.name}"/>
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134 <data name="power_out" format="tiff" label="power_${movie.name}"/>
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135 <data name="amplitude_out" format="tiff" label="amplitude_${movie.name}"/>
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136 <data name="preprocessed_out" format="tiff" label="preproc_${movie.name}">
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137 <filter>save_preprocessed['selection'] == 'Yes'</filter>
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138 </data>
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139
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140 <data name="log" format="txt" label="log_${movie.name}.txt"/>
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141 <data format="html" name="html_out" label="Report_${movie.name}"/>
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142
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143 </outputs>
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144
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145 <tests>
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146 <test>
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147 <param name="movie" value="test_movie.tif" ftype="tiff"/>
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148 <output name="phase_out" file="phase_out.tif" ftype="tiff" compare="sim_size"/>
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149 <output name="period_out" file="period_out.tif" ftype="tiff" compare="sim_size"/>
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150 <output name="power_out" file="power_out.tif" ftype="tiff" compare="sim_size"/>
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151 <output name="amplitude_out" file="amplitude_out.tif" ftype="tiff" compare="sim_size"/>
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152 </test>
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153 </tests>
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154 <help><![CDATA[
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155 **What it does**
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156
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157 Wavelet transforms a 3d-image stack (time,Y,X) pixel by pixel and extracts/evaluates the wavelet ridge. Removal of low-frequency trends is provided via sinc filtering.
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158 There are four output movies generated (phase, period, amplitude and power). They have exactly the same dimensions (time,Y,X) as the (rescaled) input.
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159
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160 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable.
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161
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162 To limit the number of Wavelet transformations (computing time), downscaling of the input movie resolution is recommended.
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163 Trimming away parts of the movie with no relevant data (e.g. outer dark edges) also speeds up the processing.
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164
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165 If multiple channels are present in your data, extract the channel of interest beforehand (e.g. with Fiji).
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166
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167 **Author**: Gregor Mönke (gregor.moenke@embl.de).
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168
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169 **Wrapper by**: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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170
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171 **Know what you are doing**
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172
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173 .. class:: warningmark
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174
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175 You will want to have understood the basics of time-frequency analysis with Wavelets, find more information about the analysis strategy employed at https://github.com/tensionhead/pyBOAT
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176
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177 **Parameter List**
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178
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179 - Sigma:
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180
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181 The Kernel bandwidth (in pixels) for the Gaussian kernels to use for pre-smoothing the input data. The default value of zero means that no pre-smoothing is done. Set this number to a desired kernel width to turn on pre-smoothing.
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182
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183 - Rescale factor:
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184
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185 Given in %, downsamples the spatial resolution of the input movie. This speeds
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186 up the whole analysis by a lot.
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187
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188 - Sampling interval:
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189
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190 Time passed between consecutive measurements, e.g 'an image every 10 minutes'.
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191
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192 - Smallest Period:
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193
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194 The minimal period to scan for, this is the higher (in frequency) end of the spectrum. A warning will be given during processing if the chosen value deceeds the Nyquist limit (2 times the sampling interval).
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195
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196 - Largest period:
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197
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198 The maximal period to scan for, this is the lower (in frequency) end of the spectrum. The inbuild Sinc filter will remove any periods larger than this form the data. Due to the 'roll off' of the filter, this value should be chosen generously. A warning will be given during processing if the chosen value exceeds the length of the time series.
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199
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200 - Number of periods to scan for:
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201
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202 This is the the number of convolutions computed per pixel.
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203
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204 Spectral resolution = ( biggest period - smallest period ) / number of periods
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205
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206 - Tcutoff:
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207
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208 The cut-off period for the sinc filter, periods larger than this one will
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209 be removed from the signal before the transform. If no value is given,
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210 no detrending is performed. At least a gracious cut-off of around ~3 times
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211 the largest period to be expected is recommended.
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212
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213 - Sliding window size
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214
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215 Length (in time units, e.g. hours) of the sliding window to estimate
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216 an amplitude envelope. The signal then gets normalized by this envelope,
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217 meaning that all amplitudes will be around ~1 after the transform. The
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218 advantage is that signal with strong amplitude trends will have more
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219 meaningful Wavelet powers after normalization.
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220
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221 ]]></help>
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222 </tool>